Hi Jiten,
You should neutralize your system, particularly if you use PBC. If the
system doesn't have a neutral charge, then when you replicate it using PBC, the
total charge would become infinity.
Cheers,
Bimo
> Thanks for the discussion on MD at different pH. When we assign the
> charges
> on the residues at different pH the total charge of the protein would be
> changed. According the sander MD simulations, it would force plasma charge
> neutrailty. In such case should we need to neutalise the systems with
> counterions before the simulation - I mean using xleap.
>
> Your advice to me would be highly appreciated, Thanks in advance.
>
> Jiten
--
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Received on Sat Mar 06 2004 - 12:53:01 PST
